Transcription profiling of rat liver exposed to methapyrilene - ILSI-HESI Hepatotoxicity Study: methapyrilene
ABSTRACT: This study examines the effects of an hepatotoxicant, Methapyrilene (CAS:91-80-5, CHEBI:6820). on hepatic gene expression in the Sprague-Dawley rat. Rats were treated with two dose levels of the compound for up to seven days. Gene expression profiles were generated using several different microarray platforms for an inter-laboratory comparison.
Project description:This study examines the effects to an hepatotoxicant clofibrate (CAS:637-07-0, CHEBI:3750) on hepatic gene expression in the Sprague-Dawley rat. Rats were treated with two dose levels of the compound for up to seven days. Gene expression profiles were generated using several different microarray platforms for an inter-laboratory comparison.
Project description:Newly emerged adult workers (24 hours old) were infected with 50,000 Nosema apis spores in sucrose solution. Controls were fed sucrose. Workers were maintained in cages in an incubator and collected at 2 and 7 days post-infection. Fat body tissue was dissected (eviscerated abdomen) and whole genome expression in this tissue was compared across treatments and collection time points using microarrays.
Project description:Here we present a statistically rigorous approach to quantifying microarray expression data that allows the relative effects of multiple classes of treatment to be compared and incorporates analytical methods that are common to quantitative genetics. From the magnitude of gene effects and contributions of variance components, we find that gene expression in adult flies is affected most strongly by sex, less so by genotype and only weakly by age (for 1- and 6-wk flies); in addition, sex-genotype interactions may be present for as much as 10% of the Drosophila transcriptome. This interpretation is compromised to some extent by statistical issues relating to power and experimental design. Nevertheless, we show that changes in expression as small as 1.2 fold can be highly significant. Genotypic contributions to transcriptional variance may be of a similar magnitude to those relating to some quantitative phenotypes and should be considered when assessing the significance of experimental treatments. The experimental design consisted of 24 cDNA microarrays, 6 for each combination of 2 genotypes (Oregon R and Samarkand) and the 2 sexes, involving 48 separate labeling reactions. We directly contrasted two time points, 1-wk and 6-wk adult flies, on each microarray. The dyes Cy3 and Cy5 were flipped for two of the six replicates of each genotype and sex combination. A common reference sample was not used. In total, we spotted 4,256 clones, representing a third of the genome, two-thirds of which were verified by resequencing before printing. We excluded 325 clones from the analysis because no consistent expression above background was detected.
Project description:MicroRNAs (miRNAs), a group of small non-coding RNAs, have recently become a subject of intense study. They are a class of post-transcriptional, negative regulators playing vital roles in plant development and growth. However, little is known about their regulatory roles in tree’s responses to the stressful environments incurred over its long-term growth. Here, we reported the cloning of small RNAs from abiotic stressed tissues of P. trichocarpa and the identification of 68 putative miRNA sequences that can be classified into 27 families based on sequence homology. Among them, 9 families are novel, raising the number of the known ptc-miRNA families from 33 to 42. Total 346 targets are predicted for the cloned ptc-miRNAs using penalty scores of ≤2.5 for mismatched patterns in the miRNA:mRNA duplexes as the criterion. Six selected targets are experimentally validated. The expression of a majority of the novel miRNAs is altered in response to cold, heat, salt, dehydration, and mechanical stresses. Microarray analysis of known ptc-miRNAs identified 19 additional cold stress responsive ptc-miRNAs that originate from 14 miRNA gene families. Interestingly, we found that miRNAs of the same family respond differentially to the same stress. This suggests that members of a miRNA family may have different functions. These results reveal possible roles for miRNAs in the regulatory networks associated with development and stress response and therefore critical to plant long-term growth; and provide useful information for developing trees with a greater level of stress-resistance. Keywords: microRNA, cold stress, time course MicroRNA abundance of 21 samples from 7 cold stress time point were analyzed, each cold stress time point contain three replicates. 0 hour cold stress treatment were used as control.
Project description:Newly emerged adult workers (24 hours old) were infected with 25,000 Nosema apis spores and 25,000 Nosema ceranae spores in sucrose solution. Controls were fed sucrose. Workers were maintained in cages in an incubator and collected at 14 days post-infection. Fat bodies (eviscerated abdomens) were dissected and whole genome expression in this tissue was compared across treatments using microarrays.
Project description:Newly emerged adult workers (24 hours old) were infected with 50,000 Nosema apis spores in sucrose solution. Controls were fed sucrose. Workers were maintained in cages in an incubator and collected at 1 and 2 days post-infection. Midguts were dissected and whole genome expression in this tissue was compared across treatments and collection time points using microarrays.
Project description:Phenotypic plasticity, the ability of one genotype to express different phenotypes in response to changing environmental conditions, is one of the most common phenomena characterising the living world and is not only relevant for the ecology but also for the evolution of species. Daphnia, the waterflea, is a textbook example for predator induced phenotypic plastic defences including changes in life-history, behaviour and morphology. However, the analysis of molecular mechanisms underlying these inducible defences is still in its early stages.<br><br>We exposed Daphnia magna to chemical cues of the predator Triops cancriformis to identify key processes underlying plastic defensive trait formation. D. magna is known to develop an array of morphological changes in the presence of T. cancriformis including changes of carapace morphology and cuticle hardening. To get a more comprehensive idea of this phenomenon, we studied four different genotypes originating from habitats with different predation history, reaching from predator-free to temporary habitats containing T. cancriformis.<br><br>We analysed the morphologies as well as proteomes of predator-exposed and control animals. Three genotypes showed morphological changes when the predator was present. Using a high-throughput proteomics approach, we found 294 proteins which were significantly altered in their abundance after predator exposure in a general or genotype dependant manner. Proteins connected to genotype dependant responses were related to the cuticle, protein synthesis and calcium binding whereas the yolk protein vitellogenin increased in abundance in all genotypes, indicating their involvement in a more general response. Furthermore, genotype dependant responses at the proteome level correlated well with local adaptation to Triops predation.<br><br>Altogether, our study provides new insights concerning genotype dependant and general molecular processes involved in predator-induced phenotypic plasticity in D. magna.